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Chapter 1: The Chemical nature of the Cell
The Cell theory states that:
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all living things are composed of cells and the products of cells
cells are the basic functional unit of living things
all cells arise from pre-existing cells
Each cell is a highly organised assembly of atoms and molecules, which interact in
thousands of chemical reactions. Cells can be likened to chemical factory.
The cell – a chemical factory
Terms:
Element: a pure substance made up of only one type of atom
Compound: a substance made up of two or more elements that have chemically
combined
Atom: the smallest particle of an element
Molecule: smallest particle of a compound (or element)
Isotope: atoms of an element that have extra neutrons. Emit radiation.
Matter has mass and takes up space; it consists of particles called atoms. Each atom
has a nucleus containing protons (+) and neutrons (0). Negatively charged
electrons (-) spin around the nucleus in regions of space known as orbitals.
All living things are composed of chemicals. These chemicals fall into two
categories:
1.
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Organic chemicals are complex carbon containing molecules
Proteins
Carbohydrates
Lipids
Nucleic acids
2.
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Inorganic chemicals do not contain carbon in a complex form
Water H2O
Carbon dioxide CO2
Oxygen O2
Mineral ions such as: K+,Cl-,Mg2+,NO3- etc
Polar molecules: have an uneven distribution of charge giving it distinct charged
ends
Non-polar molecules: disperses the charge evenly; it lacks charged ends
Water is a polar molecule, with negatively and positively charged ends.
This property means that water can interact with other charged particles, such as
polar molecules or ions (e.g. Na+, NO3- etc).
Polar substances can form H bonds with polar molecules of water and so dissolve –
they are called hydrophilic (water loving)
Non-polar substances will not dissolve in water because they cannot form H bonds
with water – they are hydrophobic.
Rule for substances to form a solution: ‘like dissolves like’
Biological macromolecules
Biological macromolecules (or biomacromolecules) are large molecules that have
important functional and structural roles in cells.
There are 4 classes of biomacromolecules:
1.
2.
3.
4.
Proteins
Nucleic Acids
Carbohydrates
Lipids
Each kind of biomacromolecule has characteristics or properties that make it
effective for carrying out its particular function: that is the structure and properties
suit the purpose.
The synthesis of biomacromolecules
Autotrophs: organisms that are able to synthesise their own biomacromolecules
from inorganic compounds.
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Plants and algae  photosynthesis
Certain species of bacteria use the energy released from areas of geothermal
activity  chemosynthetic bacteria
Heterotrophs: synthesise their own biomacromolecules from organic molecules they
have ingested.
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animals
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fungi
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majority of bacteria
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many protists
Making a polymer (polymerisation)
Biomacromolecules are synthesised inside cells. This involves linking smaller
repeating units; each called a monomer, to form large chains called polymers.
This process is known as polymerisation.
Carbohydrates, proteins and nucleic acids are made up of interlinked subunits, and
therefore are called polymers.
Note: Lipids are not polymers as they are composed of distinct chemical
groups of atoms.
Monomers link together when the hydroxyl (-OH) group of one monomer reacts
with the hydrogen of another monomer, forming a water molecule. This reaction is
called condensation polymerisation.
Carbohydrates
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Most common compounds in living things
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Composed of C, H and O in ratio: nCH2O
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Classified as:
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Monosaccharides (simple sugars)
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Disaccharides
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Polysaccharides
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Important source of energy
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Important structural component (cellulose) in plants
Can combine with other substances to form important compounds e.g.
Glycoproteins (= carbohydrate + protein)
The main polysaccharides:
Starch: branched chains of glucose molecules used as a storage molecule in plants
Glycogen: branched chains of glucose used as storage molecule in animals
Cellulose: composed of glucose molecules, forms part of cell wall of plants
Chitin: forms the basis of the insect exoskeleton and cell walls of fungi. Made up of
chains of modified glucose molecules
Lipids
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diverse group of molecules that include fats and oils, phospholipids, terpenes,
waxes, glycolipids and steroids
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They are usually hydrophobic in water
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Structural component of membranes – phospholipid bi-layer
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contain C,H and O (less O than carbohydrates), and may also contain P and N
Functions of lipids
o
Energy source (X 2 [CH2O])
o
Specific biological functions, such as transmission of chemical signals within
and outside cell
o
Oils (such as found in sunflower and canola seeds) store energy and matter for
new growth
o
Fats in animals promote insulation, and acts as food reserve (e.g. polar bears);
and protect vital organs such as the kidneys (perirenal fat) and heart
(pericardial fat)
o
Terpenes in plant essential oils: give characteristic odours and flavours
o
Waxes and cutins
o
Steroids: includes steroid hormones, bile salts and cholesterol
Structure of Lipids
Lipids are classified according to their solubility, which inturn depends on their
shape and intermolecular bonding. Lipid molecules have large non-polar regions so
are hydrophobic and insoluble in water.
1.
Triglycerides: fats and oils of plants and animals are composed of
triglyceride molecules. These molecules consist of three fatty acids attached to
a glycerol backbone.
a.
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b.
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Saturated fatty acids (animal fat):
Single bond between carbon atoms and maximum number of H atoms
attached to each C.
Solid: examples include lard, butter, fats and blubber
Unsaturated fatty acids (plant):
Double bonds between some C atoms. Do not have maximum number of H
atoms with C atoms
Oils: example include canola, sunflower, olive and aromatic oils of plants
Lipids in the membranes of cells
1.
Phospholipids: form when a phosphate group is added to the glycerol rather
than a third fatty acid. The phosphate region is hydrophilic, whereas the fatty
acid tails are hydrophobic so these molecules form lipid bi-layers that make
up the cell membranes.
2.
Glycolipids: form when a carbohydrate attaches to the glycerol backbone
rather than a third fatty acid. Important in communication as found
projecting from cells. Detect and bind with signalling molecules.
3.
Cholesterol: component of cell membranes (except inner membrane of
mitochondria and chloroplasts) and of myelin around nerves. Belong to a
group of lipids known as steroids.
Important for/as:
 maintaining level of firmness in cell membrane
 starting point for synthesis of steroid hormones: vitamin D,
testosterone and oestrogen
 bile synthesis
Proteins
Consist of:
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structural proteins: a vital structural component of all cells, and hence body
tissues, organs and systems
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functional proteins: the intracellular and extracellular enzymes, hormones and
many other substances.
Proteome: the structure and properties of all the proteins produced by an
organism’s genome (genetic material)
Proteomics: the study of the structure and function of proteins, including the
way they work and interact with each other
The basic building blocks of proteins are amino acids.
Amino Acids
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There are 20 amino acids
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All amino contain:
o
An amino (amine) group (NH2)
o
A carboxylic acid group (COOH)
o
R group
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The difference in the R group distinguishes one amino acid from another and
determines its properties
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Some R groups give the protein molecule polar regions, and other groups
make regions non-polar.
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Non-polar hydrophobic regions are tucked away within the protein, away
from water molecules; whereas polar hydrophilic regions tend to be on the
surface of the protein exposed to water molecules
From amino acids to proteins
The process of synthesising protein molecules can be explained by the 4 levels that
give rise to the final structure:
1.
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Primary structure:
the amino acid sequence in the polypeptide
amino acids bond together in the process of condensation polymerisation and
each bond between 2 amino acids is termed a peptide bond
2.
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3.
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4.
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Secondary structure:
refers to the coiling and folding the polypeptide chain undergoes once it is
formed
occurs due to H bonding occurring between particular AA
o
α – helices: tight coils
o
β – sheets: folding forms
o
random loops: unchanged
β – sheets and random loops form the basis of the active site in enzymes
Tertiary structure
Hydrophilic R groups attract other hydrophilic R groups according to the ‘like
attracts like’ rule
This interaction causes the polypeptide chain to fold, coil or twist into the
proteins functional shape or conformation.
The interaction between the R groups of amino acids result in H bonds, ionic
bonds or disulfide bridges between adjacent cysteine acids.
It is the tertiary structure of the protein which determines its function
Quaternary structure
Refers to biologically active proteins that consist of more than on polypeptide
chain; held together by the interactions between atoms in the separate
polypeptide chains. Antibodies consist of 4 PP chains held together by
disulphide bonds
Nucleic Acids
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large polymers made up of nucleotides
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carry genetic or heredity information in cells (DNA and RNA) and involved
in protein synthesis (RNA)
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Deoxyribosenucleic acid (DNA) and Ribonucleic acid (RNA) are the two
nucleic acids
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DNA is double stranded, RNA is single stranded
Nucleotides
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monomers of nucleotides
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Each nucleotide has:
o
o
o
o
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5 carbon sugar (ribose in RNA; deoxyribose in DNA)
Negatively charged phosphate group
An inorganic N containing base
There are 4 bases in DNA:
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Adenine (A)
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Thymine (T)
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Guanine (G)
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Cytosine (C)
In each nucleotide strand the sugar molecule of one nucleotide binds with the
phosphate group of the next nucleotide, leaving the base sticking out from
the sugar
Each nucleotide links together in 5' to 3' to form long polymers; that is the
phosphate group attached to the 5' carbon of one ribose monomer bonds to
the hydroxyl group attached to the 3' of another ribose monomer forming a
phosphodiester bond
In this reaction the H from the sugar and hydroxyl from the phosphate
‘condense’ out as a water molecule
DNA
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H bonds between complementary bases in each strand, create the rungs in the
ladder, which link the two nucleotide strands together
o
A:T
o
G:C
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This forms a twisted ladder or spiral staircase; the double helix
RNA
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single stranded
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ribose sugar has one less oxygen than deoxyribose in DNA
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T (in DNA) replaced with Uracil (U)
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mRNA carries gene information to ribosomes in cytoplasm (either free
floating or attached to ER (Rough ER); coding for protein synthesis
The function of DNA
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Segment of DNA on a chromosome that codes for a particular protein =
GENE
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Each sequence of three bases forms a triplet code; which in turn codes for a
particular amino acid
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mRNA takes the genetic information contained in the base sequence of a
gene, from the nucleus to a ribosome
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Here the base sequences are ‘read’ three bases at a time; that is in codons
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The ribosomes are composed of proteins + rRNA
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The incoming amino acids are attached to tRNA
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Each tRNA has an anticodon that is complementary to a specific codon on
mRNA
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The amino acids then interlink in precise sequence determined by the triplet
code on the mRNA